Two major molecular forms of thrombomodulin fragments present in urine were isolated from human urine by four sequential steps of column chromatography. The apparent molecular weights of these thrombomodulins estimated by sodium dodecyl sulfate polyacrylamide gel electrophoresis were 98, 000 (type I) and 90, 000 (type II) with dithiothreitol, and 60, 000 (type I) and 55, 000 (type II) without dithiothreitol. The isoelectric points of the type I and type II molecules were 2.5 and 3.8, respectively. From sequence analyses, both forms were revealed to have identical 468 amino acid sequences, Ala1-Asp468, lacking 29 amino acids of the carboxyl-terminal sequence of intact cellular thrombomodulin. Major structural differences between type I and type II were observed in the carbohydrate composition: type II had less galactosamine content than type I. Both types were active in thrombin inhibition and protein C activation, although the activities were significantly less than those of intact cellular thrombomodulin. Type I had twice as much inhibitory activity on thrombin clotting activity as type II, whereas type II was more effective as a cofactor for thrombin-catalyzed protein C activation than type I.